Schematic drawing tool (also used in Intel Quartus Prime

A lot going on here.

First, I think you mean .bdf, not GDF. That's a schematic design file.

Second, if you are using Quartus Pro, you can no longer create a schematic design. Schematic design is still supported in Lite and Standard.

Speaking of which, Lite is the free version of Quartus. You don't indicate what you've downloaded or installed, but if you need the free version, it's Lite. It supports the whole process of design, compilation, and device programming for the devices it supports.

If you have a .bdf and it's set as your top-level design file, you can just compile the project. I'm not sure what you are referring to about organizing the gates. Just run a full compilation.

As for adding flip-flops or any other basic logic to a schematic, just double-click in any blank space in the schematic and choose a flip-flop (D or otherwise) from the symbol library. I'm not sure what you're talking about regarding drawing shapes.